BN0615 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 2 2.1067e-06 6.9369e-04
Layer 3 8.2010e-06 1.2274e-03
Layer 1 5.6953e-05 2.8438e-03
Layer 4 1.5787e-04 5.9298e-04
Layer 5 3.6549e-04 1.0934e-03
Layer 6 8.9317e-04 3.7236e-03
WM 2.6241e-02 1.9231e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
RAB3A Expression Distribution
Gene Specificity Score (GSS)
RAB3A GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
RAB3A Layer 4 2.7539 0.7829
SNCA Layer 5 2.6602 0.7767
TMEM130 Layer 2 2.5840 0.7724
GRIN1 Layer 3 2.8281 0.7724
PDP1 Layer 2 2.5781 0.7711
NELL2 Layer 2 2.7305 0.7702
ATP1A3 Layer 5 2.9248 0.7695
ATP2A2 Layer 1 2.7129 0.7695
EGR1 Layer 2 3.1113 0.7694
EGR3 Layer 2 3.4609 0.7691
TAGLN3 Layer 2 2.6895 0.7675
NPTXR Layer 2 3.2148 0.7664
SPTAN1 Layer 5 2.6367 0.7657
RGS4 Layer 5 2.9160 0.7652
GABRG2 Layer 2 3.0195 0.7649
HSPA8 Layer 4 2.8428 0.7638
SH3GL2 Layer 4 3.1523 0.7636
GABRA1 Layer 3 2.8994 0.7633
BEX1 Layer 2 2.5273 0.7632
NCDN Layer 2 2.9277 0.7613
BMERB1 Layer 4 2.7969 0.7612
CAMK1D Layer 2 2.7129 0.7610
NDRG4 Layer 5 2.7998 0.7609
GRASP Layer 2 2.7480 0.7608
CPLX2 Layer 1 3.1055 0.7605
ISCU Layer 4 2.4941 0.7604
HPCAL4 Layer 2 2.5723 0.7596
PTPRN Layer 5 2.6543 0.7589
CALY Layer 3 2.7334 0.7588
CAMK2A Layer 2 3.3066 0.7587
CEND1 Layer 4 2.6631 0.7586
NEFM Layer 3 3.2227 0.7582
PPP2R1A Layer 2 2.5215 0.7581
PAK1 Layer 2 2.9082 0.7571
PHYHIP Layer 2 2.8398 0.7566
PNMA2 Layer 4 2.7969 0.7557
BSCL2 Layer 2 2.6367 0.7545
CCK Layer 2 2.8027 0.7542
BEX2 Layer 2 2.6660 0.7542
PACSIN1 Layer 2 2.6543 0.7540
STXBP1 Layer 4 2.6367 0.7537
NPTN Layer 2 2.7539 0.7536
NSF Layer 3 2.8340 0.7535
SYN1 Layer 4 2.8711 0.7534
MDH1 Layer 4 2.5361 0.7528
MAPK1 Layer 2 3.0195 0.7523
RIMS3 Layer 4 2.5986 0.7522
NCS1 Layer 2 2.7129 0.7518
PI4KA Layer 5 2.7783 0.7511
ATP1A1 Layer 2 2.9668 0.7499

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0615
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0615_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0615/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0615/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0615/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0615/report/PD/BN0615_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0615/report/PD/BN0615_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 00:41:07
  • Number of Processes: 10
  • Spending Time: 0h 4m